Modular decomposition of protein-protein interaction networks
Open Access
- 21 July 2004
- journal article
- Published by Springer Nature in Genome Biology
- Vol. 5 (8) , R57
- https://doi.org/10.1186/gb-2004-5-8-r57
Abstract
We introduce an algorithmic method, termed modular decomposition, that defines the organization of protein-interaction networks as a hierarchy of nested modules. Modular decomposition derives the logical rules of how to combine proteins into the actual functional complexes by identifying groups of proteins acting as a single unit (sub-complexes) and those that can be alternatively exchanged in a set of similar complexes. The method is applied to experimental data on the pro-inflammatory tumor necrosis factor-alpha (TNF-alpha)/NFkappaB transcription factor pathway.Keywords
This publication has 34 references indexed in Scilit:
- Protein complexes and functional modules in molecular networksProceedings of the National Academy of Sciences, 2003
- Module networks: identifying regulatory modules and their condition-specific regulators from gene expression dataNature Genetics, 2003
- Network Motifs: Simple Building Blocks of Complex NetworksScience, 2002
- Analyzing yeast protein–protein interaction data obtained from different sourcesNature Biotechnology, 2002
- Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometryNature, 2002
- Functional organization of the yeast proteome by systematic analysis of protein complexesNature, 2002
- A comprehensive two-hybrid analysis to explore the yeast protein interactomeProceedings of the National Academy of Sciences, 2001
- TFIIF-TAF-RNA polymerase II connection.Genes & Development, 1994
- A novel genetic system to detect protein–protein interactionsNature, 1989
- Algorithmic aspects of the substitution decomposition in optimization over relations, set systems and Boolean functionsAnnals of Operations Research, 1985